Is there a reason why SmartRefStream has such a radically different 
interface than ReferenceStream, even though it's a direct subclass?

Yes. The reason is that you shouldn't use SmartRefStream the way 
you're using it. The "correct" way is using #fileOutClass:andObject: 
like here:

Writing:
  file := FileStream newFileNamed: 'data.obj'.
  file fileOutClass: nil "no class" andObject: data.

Reading:
  file := FileStream readOnlyFileNamed: 'data.obj'.
  data := file fileInObjectAndCode.